Method of increasing complementarity in a heteroduplex

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

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C435S091200

Reexamination Certificate

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07838219

ABSTRACT:
We describe here an in vitro method of increasing complementarity in a heteroduplex polynucleotide sequence. The method uses annealing of opposite strands to form a polynucleotide duplex with mismatches. The heteroduplex polynucleotide is combined with an effective amount of enzymes having strand cleavage activity, 3′ to 5′ exonuclease activity, and polymerase activity, and allowing sufficient time for the percentage of complementarity to be increased within the heteroduplex. Not all heteroduplex polynucleotides will necessarily have all mismatches resolved to complementarity. The resulting polynucleotide is optionally ligated. Several variant polynucleotides result. At sites where either of the opposite strands has templated recoding in the other strand, the resulting percent complementarity of the heteroduplex polynucleotide sequence is increased. The parent polynucleotides need not be cleaved into fragments prior to annealing heterologous strands. Therefore, no reassembly is required.

REFERENCES:
patent: 4994368 (1991-02-01), Goodman et al.
patent: 5459039 (1995-10-01), Modrich et al.
patent: 5556747 (1996-09-01), Kumar
patent: 5571676 (1996-11-01), Shuber
patent: 5679522 (1997-10-01), Modrich et al.
patent: 5683877 (1997-11-01), Lu-Chang et al.
patent: 5723323 (1998-03-01), Kauffman et al.
patent: 5795747 (1998-08-01), Henco et al.
patent: 5861482 (1999-01-01), Modrich et al.
patent: 5869245 (1999-02-01), Yeung et al.
patent: 5877280 (1999-03-01), Wetmur
patent: 5922539 (1999-07-01), Modrich et al.
patent: 6057103 (2000-05-01), Short
patent: 6165793 (2000-12-01), Stemmer
patent: 6391557 (2002-05-01), Yeung
patent: 6537746 (2003-03-01), Arnold et al.
patent: 6783941 (2004-08-01), Vind
patent: 6821758 (2004-11-01), Koltermann
patent: 6846655 (2005-01-01), Wagner et al.
patent: 7056740 (2006-06-01), Padgett et al.
patent: 7078211 (2006-07-01), Padgett et al.
patent: 7217514 (2007-05-01), Padgett et al.
patent: 7235386 (2007-06-01), Padgett et al.
patent: 2002/0045175 (2002-04-01), Wang et al.
patent: 2002/0146732 (2002-10-01), Padgett et al.
patent: 2002/0177160 (2002-11-01), Padgett et al.
patent: 2003/0017477 (2003-01-01), Vind
patent: 2003/0148315 (2003-08-01), Padgett et al.
patent: 2003/0157495 (2003-08-01), Padgett et al.
patent: 2003/0186261 (2003-10-01), Padgett et al.
patent: 2004/0048268 (2004-03-01), Delcourt et al.
patent: 2004/0091886 (2004-05-01), Moore
patent: 2004/0110130 (2004-06-01), Padgett et al.
patent: 2006/0194288 (2006-08-01), Padgett et al.
patent: 2008/0145913 (2008-06-01), Padgett et al.
patent: 4112440 (1992-10-01), None
patent: 19953854 (2001-05-01), None
patent: 2789696 (2000-08-01), None
patent: WO 92/18645 (1992-10-01), None
patent: WO 93/20233 (1993-10-01), None
patent: WO 96/40902 (1996-12-01), None
patent: WO 97/37011 (1997-10-01), None
patent: WO 97/46701 (1997-12-01), None
patent: WO 99/28451 (1999-06-01), None
patent: WO 99/29902 (1999-06-01), None
patent: WO 00/71730 (2000-11-01), None
patent: WO 01/34835 (2001-05-01), None
patent: WO 01/62974 (2001-08-01), None
patent: WO-0164864 (2001-09-01), None
patent: WO 02/24953 (2002-03-01), None
patent: WO 02/079468 (2002-10-01), None
patent: WO-02092815 (2002-11-01), None
patent: WO 03066809 (2003-08-01), None
patent: WO 2004/035771 (2004-04-01), None
Dalbadie-McFarland et al. Oligonucleotide-directed mutagenesis as a general and powerful method for studies of protein function. Proceedings of the National Academy of Sciences, USA 79: 6409-6413 (1982).
Oleykowski, et al., “Mutation detection using a novel plant endonuclease”,Nucleic Acids Research, 1998, vol. 26, No. 20, pp. 4597-4602, Oxford University Press, United Kingdom.
Oleykowski, et al., “Incision at Nucleotide Insertions/Deletions and Base Pair Mismatches by the SP Nuclease of Spinach”,Biochemistry, 1999, vol. 38, pp. 2200-2205, American Chemical Society, Columbus, OH.
Biswas and Hsieh, “Identification and characterization of a thermostable MutS homolog fromThermus aquaticus”, J. Biol. Chem.(1996) 271(9):5040-5048.
Kraemer and Digiovanna, “Topical enzyme therapy for skin diseases?”,J. Am. Acad. Dermatol.(2002) 46:463-6.
O'Grady, et al., “DNA repair in thermophiles: investigation of DNA-binding activities inThermus aquaticus”, Biochem. Soc. Tranactions(1997) 25:319-22.
Sugahara, et al., “Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile,Thermus thermophilusHB8”,EMBO J(2000) 19(15):3857-3869.
Wang, “Creating hybrid genes by homologous recombination”,Disease Markers(2000) 16:3-13.
Birkenkamp and Kemper, “In vitro processing of heteroduplex loops and mismatches by Endonuclease VII”,DNA Research, 1995, vol. 2, pp. 9-14.
Abastado, et al., “Processing of complex heteroduplexes inEscherichia coliandCos-1 monkey cells”,Proc. Natl. Acad. Sci. USA, Sep. 1984, vol. 81, pp. 5792-5796.
Cami, et al., “Correction of complex heteroduplexes made of mouse H-2 gene sequences inEscherichia coliK-12”,Proc. Natl. Acad. Sci. USA, Jan. 1984, vol. 81, pp. 503-507.
Chang, et al, “Recombination following transformation ofEscherichia coliby heteroduplex plasmid DNA molecules”,Gene, 1984, vol. 29, pp. 255-261, Elsevier.
Cotton, “Slowly but surely towards better scanning for mutations”,TIG, Feb. 1997, vol. 13, No. 2, pp. 43-46, Elsevier Science Ltd.
Joyce, “Directed Molecular Evolution”,Scientific American, Dec. 1992, pp. 90-97.
Kulinski, et al., “CEL I Enzymatic Mutation Detection Assay”,Biotechniques, Jul. 2000, vol. 29, pp. 44-48.
Lahue, et al., “Requirement for d(GATC) sequences inEscherichia coli mutHLSmismatch correction”,Proc. Natl. Acad. Sci. USA, Mar. 1987, vol. 84, pp. 1482-1486.
Modrich, “Strand-specific Mismatch Repair in Mammalian Cells”,The Journal of Biological Chemistry, Oct. 3, 1997, vol. 272, No. 4, pp. 24727-24730, The American Society of for Biochemistry and Molecular Biology, Inc., Bethesda, MD.
Oleykowski, et al., “Mutation detection using a novel plant endonuclease”,Nucleic Acids Research, 1998, vol. 26, No. 20, pp. 4597-4602, Oxford University Press, United Kingdom.
Oleykowski, et al., “Incision at Nucleotide Insertions/Deletions and Base Pair Mismatches by the SP Nuclease of Spinach”,Biochemistry, 1999, vol. 38, pp. 2200-2205, American Chemical Society, Columbus. OH.
Robertson, “Directed evolution patent could have major impact”,Nature Biotechnology, May 1998, vol. 16, p. 411.
Solaro, et al., “Endonuclease VII of Phage T4 Triggers Mismatch Correction in Vitro”,J. Mol. Biol., 1993, vol. 230, pp. 868-877, Academic Press Limited.
Volkov, et al., “Random Chimeragenesis by Heteroduplex Recombination”,Methods in Enzymology, 2000, vol. 328, pp. 456-463, Academic Press.
Volkov, et al., “Recombination and chimeragenesis by in vitro heteroduplex formation and in vivo repair”,Nucleic Acids Research, 1999, vol. 27, No. 18, pp. e18 (i-vi), Oxford Univeristv Press.
Yang, et al., “Purification, Cloning, and Characterization of the CEL I Nuclease”,Biochemistry, 2000, vol. 39, pp. 3533-3541; American Chemical Society.
Solaro, et al., “Endonuclease VII of Phage T4 Triggers Mismatch Correction in Vitro”,J. Mol. Biol., 1993, vol. 230, pp. 868-877, Academic Press Limited.
Yang, et al., “Purification, Cloning, and Characterization of the CEL I Nuclease”,Biochemistry, 2000, vol. 39, pp. 3533-3541, American Chemical Society.
Kulinski, et al., “CEL I Enzymatic Mutation Detection Assay”,Biotechniques, Jul. 2000, vol. 29, pp. 44-48.
Fishel, R. and R. Kolodner, Gene coversion inEscherichia coli: the recF pathway for resolution of heteroduplex DNA. J Bacteriol, 1989. 171(6): p. 3046-52.
Fishel, R.A. and R. Kolodner, AnEscherichia colicell-free system that catalyzes the repair of symmetrically methylated heteroduplex DNA. Cold Spring Herb Symp Qu

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